Abstract

The group of vertebrates includes diverse evolutionary lineages, and typical laboratory‐model vertebrates are confined to
only limited groups (tetrapods and teleost fishes) of its entire diversity. Accumulating information of the molecular sequence
for the still‐missing lineages including jawless fishes can now provide deeper insights into the definition of the taxon Vertebrata
at the genomic level. Above all, the so‐called two‐round whole genome duplications are described to have occurred in the early
vertebrate evolution. Recent molecular phylogenetic analyses for some gene families resulted in a scenario in which the genome
expansion might have been completed before the split of the lineage of cyclostomes (extant jawless fishes including hagfishes
and lampreys) from the future jawed vertebrate lineage. In addition to this genome expansion, key features of genomic contents
of the vertebrate ancestor are inferable, provided secondary changes introduced later in individual lineages are taken into
deep consideration in ancestral phylogenetic reconstruction.

Alternative scenarios about the timing of the two‐round whole genome duplications. The arrows indicate the timing of the whole
genome duplications.

Figure 2.

Identification of the genes involved in the endothelin system. Black vertical or diagonal lines indicate orthology between
species. Identification of the genes in the lamprey and the cartilaginous fishes, as well as their nomenclature, is based
on the author's previous study (Kuraku et al., ). Only the putative amphioxus ortholog of the endothelin receptors has been identified in its genome assembly and remains
to be functionally characterised. Although the EdnrB2 is shown here as present in tetrapods, its ortholog was likely lost in the lineage leading to eutherian mammals (Braasch
et al., ). The genes which were not identified within the taxonomic clades including species with sequenced genomes are indicated
as ‘not found’. The node corresponding to the common ancestor of all extant vertebrates is shown with an open circle in the
tree on the left.